AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i122_Arsenical_Resistance_Pump_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -x5 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	arsR	300	transcriptional repressor of chromosomal ars operon

Motif number 1

    CCCTCCGCCAGCTGAAGAAATCGCTA	1	7	1	GCCAGCTGAA	    0.987218	-294
GTTCTTATCTAACAGCTCAATACTATTAGC	1	59	0	AACAGCTCAA	    0.981887	-242
AGCCAGAGCCACCAACTCAGGGCTGGAAAG	1	100	1	ACCAACTCAG	    0.991623	-201
AAAGTAAAAAACCGACGCAAAGTCGGTTTT	1	126	1	ACCGACGCAA	    0.981596	-175
CAAATGAATAGCCAACTCAAAATTCACACC	1	182	1	GCCAACTCAA	    0.996486	-119
          **********

Masking position 9
Map Score:   5.60578

Number of sites scoring better than the average of aligned sites = 368
Number in coding regions = 345
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 2

ACATTGCAAGAATTAGCGATTTCTTCAGCTG	1	19	0	AATTAGCGTT	     0.81352	-282
CAATACTATTAGCCAGTGGCTAACATTGCAA	1	41	0	AGCCAGTGCT	    0.674024	-260
TCCAGCCCTGAGTTGGTGGCTCTGGCTGGAG	1	96	0	AGTTGGTGCT	    0.970018	-205
ACCGACTTTGCGTCGGTTTTTTACTTTCCAG	1	122	0	CGTCGGTTTT	    0.954321	-179
ACCGACGCAAAGTCGGTTTTTTTACGTCCTG	1	136	1	AGTCGGTTTT	    0.984847	-165
GTGAATTTTGAGTTGGCTATTCATTTGAAAG	1	178	0	AGTTGGCTTT	    0.973239	-123
TGATTGTTGCAGGTAGTGTCTCTCTTCGAAG	1	270	0	AGGTAGTGCT	    0.955849	-31
          ******** **

Masking position 11
Map Score:   4.24078

Number of sites scoring better than the average of aligned sites = 859
Number in coding regions = 795
Number in noncoding regions = 64
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 3

       CCCTCCGCCAGCTGAAGAAATCG	1	4	1	TCCGCCAGCT	    0.991426	-297
TGCAATGTTAGCCACTGGCTAATAGTATTG	1	42	1	GCCACTGGCT	    0.991426	-259
AGAGTTCTTATCTAACAGCTCAATACTATT	1	62	0	TCTAACAGCT	    0.904079	-239
TCCAGCCAGAGCCACCAACTCAGGGCTGGA	1	97	1	GCCACCAACT	    0.993177	-204
TTCGAAGAGAGACACTACCTGCAACAATCA	1	271	1	GACACTACCT	    0.948317	-30
          **********

Masking position 10
Map Score:   1.8463

Number of sites scoring better than the average of aligned sites = 2171
Number in coding regions = 2097
Number in noncoding regions = 74
Number of orfs with sites within 600 bp upstream = 83
Fraction of orfs with sites within 600 bp upstream = 0.0133312


Motif number 4

TGGAAAGTAAAAAACCGACGCAAAGTCGGT	1	123	1	AAAACCGACG	    0.994095	-178
AGGACGTAAAAAAACCGACTTTGCGTCGGT	1	136	0	AAAACCGACT	    0.995032	-165
TTTCAAATGAATAGCCAACTCAAAATTCAC	1	179	1	ATAGCCAACT	    0.972224	-122
          **********

Masking position 3
Map Score:   0.807304

Number of sites scoring better than the average of aligned sites = 101
Number in coding regions = 84
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 5

CCACCAACTCAGGGCTGGAAAGTAAAAAAC	1	108	1	AGGGCTGGAA	    0.987065	-193
ATTTGAAAGGAGGTCTGAATCAGGACGTAA	1	157	0	AGGTCTGAAT	    0.994777	-144
GGAAGGTAATAGGTGTGAATTTTGAGTTGG	1	193	0	AGGTGTGAAT	     0.99043	-108
          **********

Masking position 9
Map Score:   0.807304

Number of sites scoring better than the average of aligned sites = 83
Number in coding regions = 77
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 6

          **********

No masking
Map Score:   7.91135e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 7

          **********

No masking
Map Score:   7.91135e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 8

          **********

No masking
Map Score:   7.91135e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0